Research Project 2

Develop an improved adaptative sampling method for Nanopore dRNA and cDNA sequencing

About the Project

University of Nottingham

Nottingham, UK

Oxford Nanopore Technologies

Oxford, UK

Satrio Benowo

Early Stage Researcher

Matt Loose

Aino Järvelin

Supervisors

University of Nottingham

PhD enrolment

Research Objectives

Little is known about transcriptome-wide epi-transcriptomic  modifications and isoform diversity, especially of low abundance and biomedically relevant transcripts. Adaptive sampling (AS) is a strategy to enrich for specific transcripts in silico but its use in native RNA (dRNA) applications remains to be explored. Our objectives are:

  • To test and further develop experimental and informatic tools for adaptive sampling on RNA.
  • To demonstrate the utility of dRNA sequencing, enhanced by adaptive sampling, on analysis of RNA  isoforms, tail lengths, and modifications.
  • To apply these approaches to characterise transcriptome changes in a cancer cell line.

Envisioned Secondments

  • Wobble (Kuo): Methods for cDNA normalisation and rare transcript annotation.
  • CRG (Novoa): Epitranscriptomics data generation analysis.
  • CSIC (Conesa): Learn statistics.

Early Stage Researcher

Satrio Benowo

Nanopore,
UK

I am a researcher from Indonesia. I completed my Bachelor’s degree in biology at the Universitas Pendidikan Indonesia. My work has been focused on implementing precision medicine in healthcare. I previously collaborated with a startup company to develop affordable molecular diagnostics for colorectal cancer. Later, I worked as bioinformatics engineer for the Indonesian government, supporting a genomics project in healthcare.

I firmly believe that long-read sequencing technologies play a crucial role in uncovering novel discoveries related to human health, especially in the fields of genomics and transcriptomics. Given that the LongTREC project centers around Long-read sequencing (lrRNA-seq) and involves lrRNA-seq leaders in Europe, I am enthusiastic about becoming a part of LongTREC. Personally, I find the LongTREC predoctoral research project to be an unparalleled opportunity for young researchers worldwide, enabling us to learn more and make significant contributions to science while engaging with the global scientific community.

I am eager to pursue a deeper understanding on the biology of RNA, working with cutting-edge sequencing technology and data analysis, all under the guidance of lrRNA-seq experts in the UK-EU region. Through my doctoral training in LongTREC, I aspire to bring us one step closer to improving people’s lives.

About the Supervisors and Host Groups

Aino Järvelin

Nanopore,
UK

I am interested in using genomics and data science to solve biological puzzles and to advance human and environmental health. I love to design new projects, distill complex datasets into actionable and insightful patterns, and translate between people from different disciplines and backgrounds whenever I can to create something new together. I actively promote help build open and inclusive work environments that enable people to learn, grow, and communicate. You’re sure to grab my attention with a nice data viz.

My core toolkit consists of R, python, and genomics tools and databases. With a background in experimental biology, have a strong understanding of how bio(medical) data is generated and the needs of wetlab experimentalists.

Matt Loose

University of Nottingham
UK